GSR: Simulator - invertFREGENE
Attribute | Value |
---|---|
Title | invertFREGENE |
Short Description | InvertFREGENE is a forward-in-time simulator of inversions in population genetic data |
Long Description | invertFREGENE is the forward-in-time simulator of inversions in population genetic data, while SAMPLE samples genotype and haplotype data from the output of invertFREGENE simulations based on specified individual and marker ascertainment criteria, including a continuous and case-control disease model. invertFREGENE has been developed from a beta version of the population genetic simulator FREGENE, and as a result there are a small number of features not included in invertFREGENE (eg. it does not model natural selection), therefore we provide self-contained documentation for invertFREGENE. O'Reilly PF, Coin LJ, Hoggart CJ. invertFREGENE: software for simulating inversions in population genetic data. Bioinformatics. 2010 Mar 15;26(6):838-40. |
Project Started | 2009 |
Last Release | 14 years, 5 months ago |
Homepage | http://www.ebi.ac.uk/projects/BARGEN/ |
Citations | O'Reilly PF, Coin LJ, Hoggart CJ, invertFREGENE: software for simulating inversions in population genetic data., Bioinformatics, 03-15-2010 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 05-02-2019 (1808 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, |
Variations | Biallelic Marker, Single Nucleotide Variation, Inversion and Rearrangement (Inversion), |
Simulation Method | Forward-time, |
Input | |
Data Type | |
File format | |
Output | |
Data Type | Genotype or Sequence, Phenotypic Trait (Using sample), Demographic, Diversity Measures, |
Sequencing Reads | |
File Format | Program Specific, |
Sample Type | Random or Independent, Case-control (Using sample), |
Phenotype | |
Trait Type | Quantitative (Using sample), |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Bottleneck (Using consecutive invertfregene simulations), User Defined (Using consecutive invertfregene simulations), |
Gene Flow | Island Models, User-defined Matrix, |
Spatiality | |
Life Cycle | |
Mating System | Random Mating, |
Fecundity | |
Natural Selection | |
Determinant | Single-locus, Multi-locus, |
Models | Multi-locus models, |
Recombination | Uniform, Varying Recombination Rates, Gene Conversion Allowed, |
Mutation Models | Two-allele Mutation Model, |
Events Allowed | |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Linux and Unix, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using invertFREGENE has been provided.
Please propose new citations if you are aware of publications that use this software.